Apr 28 2020
[ RIDE Setup ]
RIDE is a fast 3D molecular similarity search method based on Atomic Property Fields, developed at MolSoft. RIDE searches databases of compound conformers for molecules that are isosteric to the query, i.e. have similar 3D configurations and distributions of atomic properties.
GPU-based implementation is capable of searching ~0.5mln conformers/second on a single GPU card and perform 3D virtual screens of millions of compounds with the level of interactivity comparable to 2D searches. VLS benchmarking on DUDe indicates that RIDE searches produce enrichments on par with much slower standard flexible APF VLS.
RIDE applications include:
A simple web-based interface is provided for the ease of use by chemists, or can be used in the ICM-Pro software. In either format, RIDE allows fine-tuning of the queries to generate most desirable hit lists. This includes:
Prepare the template to search against:
Download the pre-converted 3D database for screening:
GPU-enabled RIDE server can be installed from Docker container (instructions are contained in download)
After the Docker is installed -paste the URL into URL box, press refresh button next to the database combo to refresh DB list.
Other parameters are the same as for local search (see above).
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